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<HR>

<H3>react command 
</H3>
<P><B>Syntax:</B>
</P>
<PRE>react style args 
</PRE>
<UL><LI>style = <I>none</I> or <I>tce</I> or <I>qk</I> or <I>tce/qk</I> 

<LI>args = arguments for that style 

<PRE>  <I>none</I> args = none
  <I>tce</I> args = infile
    infile = file with list of gas-phase chemistry reactions
  <I>qk</I> args = infile
    infile = file with list of gas-phase chemistry reactions
  <I>tce/qk</I> args = infile
    infile = file with list of gas-phase chemistry reactions
  <I>tce/kk</I> args = infile
    infile = file with list of gas-phase chemistry reactions 
</PRE>

</UL>
<P><B>Examples:</B>
</P>
<PRE>react none
react tce air.tce
react qk air.tce 
</PRE>
<P><B>Description:</B>
</P>
<P>Define chemical reactions to perform in the gas phase when
particle-particle collisions occur.  See the
<A HREF = "surf_react.html">surf_react</A> command for specification of surface
chemistry reactions.
</P>
<P>The <I>none</I> style means that no chemistry will be performed, which is
the default.
</P>
<P>For other styles, a file is specified which contains a list of
chemical reactions, with their associated parameters.  The reactions
are read into SPARTA and stored in a list.  Each time a simulation is
run via the <A HREF = "run.html">run</A> command, the list is scanned.  Only
reactions for which all the reactants and all the products are
currently defined as species-IDs will be active for the simulation.
Thus the file can contain more reactions than are used in a particular
simulation.  See the <A HREF = "species.html">species</A> command for how species
IDs are defined.
</P>
<P>The reaction models for the various styles are described below.  When
a pair of particles collide, the list of all reactions with those two
species as reactants is looped over.  A probability for each reaction
is calculated, using the formulas discussed below, and a random number
is used to decide which reaction (if any) takes place.  No check is
made that the sum of probabilities for all possible reactions is <=
1.0, but that should normally be the case if reasonable reaction
coefficients are defined.
</P>
<P>The format of the reaction file is the same for all three of the
currently defined styles, and is also described below.  The various
styles interpret and compute the specified reactions in different
ways.  The data directory in the SPARTA distribution contains reaction
files for these reaction models, all with the suffix ".tce".
</P>
<HR>

<P>The <I>tce</I> style is Bird's Total Collision Energy (TCE) model.  When
this style is specified, all computed reactions will use the TCE
model.
</P>
<P>Using kinetic theory, the TCE model allows for reaction probabilities
to be defined based on known, measured, reaction rates.  The model is
described in detail in <A HREF = "#Bird94">(Bird94)</A>; see chapter 6. The required
input parameters for each reaction (discussed below) are values that
permit its effective Arrhenius rate to be calculated, namely
</P>
<CENTER><IMG SRC = "Eqs/arrhenius.jpg">
</CENTER>
<P>where K(T) is the forward reaction rate, T is the temperature of the
participating molecules which is a function of their velocities and
internal energy states, k the Boltzmann constant, and A,b,Ea are input
parameters as discussed below.
</P>
<P>All 5 reactions coefficients read from the reaction file (described
below) are used to calculate terms in equation 6.10 of
<A HREF = "#Bird94">(Bird94)</A> for the probability that a reaction takes place.
</P>
<P>The C2, C3, C4 values are the Arrhenius activation energy Ea,
prefactor A, and exponent b, used in the rate formula above.
</P>
<HR>

<P>The <I>qk</I> style is Bird's Quantum-Kinetic model (QK).  When this style
is specified, all computed reactions will use the QK model.
</P>
<P>The QK model implemented is that of <A HREF = "#Bird09">(Bird09)</A> as validated
<A HREF = "#Gallis09">(Gallis09)</A> and modified <A HREF = "#Gallis10">(Gallis10)</A>.
</P>
<P>The QK model depends solely on properties of the colliding molecules
and unlike the TCE model makes no use of measured reaction rates or 
adjustable parameters. The macroscopic properties used in the QK model 
are the available collision energy, activation energies, and quantized
vibrational energy levels.
</P>
<P>According to the QK model dissociation reactions take place when the 
maximum obtainable vibrational energy after an inelastic energy exchange
is higher than the dissociation level <A HREF = "#Bird09">(Bird09)</A>. 
</P>
<CENTER><IMG SRC = "Eqs/qk_dissociation.jpg">
</CENTER>
<P>Exchange reactions take place when the vibrational energy after a trial 
energy exchange is above the activation energy of the exchange reaction
<A HREF = "#Gallis10">(Gallis10)</A>. 
</P>
<CENTER><IMG SRC = "Eqs/qk_exchange.jpg">
</CENTER>
<P>A new version of the QK model for exchange reactions has been proposed
by <A HREF = "#Bird11">(Bird11)</A>.  This will be implemented in future releases of
SPARTA.
</P>
<P>For the QK model, SPARTA reads the same 5 coefficients per reaction
from the reaction file (described below) as for the TCE model.  Three
of the coefficients (C1,C2,C5) are used to calculate terms in equation
6.10 of <A HREF = "#Bird94">(Bird94)</A> for the probability that a reaction takes
place.  The Arrhenius rate parameters C3 and C4 are ignored by the QK
model.
</P>
<HR>

<P>The <I>tce/qk</I> style is a hybrid model which can be used to compute
reactions using both the TCE and QK models.  When this style is
specified, reactions from the input file that are flagged with an A =
Arrhenius style will be computed using the TCE model.  Reactions from
the input file that are flagged with a Q = Quantum style will be
computed using the QK model.
</P>
<HR>

<P>The format of the input reaction file is as follows.  Comments or
blank lines are allowed in the file.  Comment lines start with a "#"
character.  All other entries must come in 2-line pairs with values
separated by whitespace in the following format
</P>
<PRE>R1 + R2 + ... --> P1 + P2 + ...
type style C1 C2 ... 
</PRE>
<P>The first line is a text-based description of a single reaction.  R1,
R2, etc are one or more reactants, listed as <A HREF = "species.html">species</A>
IDs.  P1, P2, etc are one or more products, also listed as
<A HREF = "species.html">species</A> IDs.  The number of allowed reactants and
products depends on the reaction type, as discussed below.  In most
cases there is no restriction on the order or listed reactants or
products on what species are listed.  Exceptions are detailed below.
Note that individual reactants and products must be separated by
whitespace and a "+" sign.  The left-hand and right-hand sides of the
equation must be separated by whitespace and "-->".
</P>
<P>The <I>type</I> of each reaction is a single character (upper or lower
case) with the following meaning.  The type determines how many
reactants and products can be specified in the first line.
</P>
<PRE>D = dissociation = 2 reactants and 3 products
E = exchange = 2 reactants and 2 products
I = ionization = 2 reactants and 2 or 3 products
R = recombination = 2 reactants and 1 product (see below) 
</PRE>
<P>A dissociation reaction means that R1 dissociates into P1 and P2 when
it collides with R2.  R2 is preserved in the collision, so P3 = R2 is
required.
</P>
<P>An exchange reaction is a collision between R1 and R2 that results in
new products P1 and P2.  There is no restriction on the species
involved in the reaction.
</P>
<P>An ionization reaction with 2 products is typically a collision
between R1 and R2 that results in a positively charged ion and an
election.  See the discussion on ambipolar reactions below.  However,
SPARTA does not check for this, so there is no restriction on the
species involved in the reaction.
</P>
<P>An ionization reaction with 3 products is typically a collision
between a neutral R1 and an electon R2 which ejects an electron from
the neutral species, resulting in an ion P1 and a new electron P2.
See the discussion on ambipolar reactions below.  Again, SPARTA does
not check for this, so there is no restriction on the species involved
in the reaction.  R2 is preserved in the collision, so P3 = R2 is
required.
</P>
<P>A recombination reaction is a collision between R1 and R2 that results
in P1.  There is no restriction on the species involved in the
reaction.
</P>
<P>Note that recombination reactions actually involve a 3rd particle
whose species is not altered by the reaction but whose velocity is, in
order to balance energy and momentum.  So conceptually it can be
thought of as both a reactant and a product.  There are 3 ways you can
specify recombination reactions, to include information about which
species of 3rd particles are eligible to participate:
</P>
<PRE>R1 + R2 -> P1
R1 + R2 -> P1 + atom/mol
R1 + R2 -> P1 + P2 
</PRE>
<P>In the first case, no info for a 3rd particle is listed.  This means
any species of 3rd particle can be used.  In the second case, a
non-species keyword is used, either "atom" or "mol".  This means the
3rd particle must be either an atomic species, or a molecular species.
This is based on the vibrational degrees of freedom listed in the
<A HREF = "species.html">species file</A>.  A non-zero DOF is molecular; zero DOF is
atomic.  In the third case, a specific species P2 is listed.  This
means the 3rd particle must be that species.
</P>
<P>Note that for the same R1 and R2, multiple recombination reactions can
be listed in the reaction file.  When two particles R1 and R2 are
selected for collision and a possible reaction, if any recombination
reaction is defined for R1 and R2, then a 3rd particle in the same
grid cell is randomly selected.  Its species P2 is used to match at
most one of the possibly multiple recombination reactions for R1 and
R2.  Only that recombination reaction is checked for a reaction as a
possible outcome of the collision.
</P>
<P>This matching is done from most-specific to least-specific, i.e. the
reverse ordering of the 3 cases above.  If there is a defined reaction
that lists P2 (third case, most specific), it is used.  If not, and
there is a defined reaction for "atom" or "mol" that corresponds to P2
(second case, intermediate specificity), then it is used.  If not, and
there is a defined reaction with no P2 (first case, least specific),
then it is used.  If none of these matches occur, no recombination
reaction is possible for that collision between R1 and R2.  Note that
these matching rules means that for the same R1 and R2, you can list
two reactions, one with P2 = "atom", and one with P2 = "mol".  And/or
you can list multiple reactions of the third kind, each with a unique
P2.
</P>
<P>IMPORTANT NOTE: If the ambipolar approximation is being used, via the
<A HREF = "fix_ambipolar.hmtl">fix ambipolar</A> and <A HREF = "collide_modify.html">collide_modify ambipolar
yes</A> commands, then reactions which involve either
ambipolar ions or the ambipolar electron have more restricitve rules
about the ordering of reactants and products.  See the next section
for a discussion of these requirements.
</P>
<P>The <I>style</I> of each reaction is a single character (upper or lower
case) with the following meaning:
</P>
<UL><LI>A = Arrhenius 
<LI>Q = Quantum 
</UL>
<P>The style determines how many reaction coefficients are listed as C1,
C2, etc, and how they are interpreted by SPARTA.
</P>
<P>For both the A = Arrhenius style and Q = Quantum style, there are 5
coefficients:
</P>
<UL><LI>C1 = number of internal degrees of freedom (as defined by the TCE model)
<LI>C2 = Arrhenius activation energy Ea
<LI>C3 = Arrhenius prefactor A
<LI>C4 = Arrhenius exponent b
<LI>C5 = overall reaction energy (positive for exothermic) 
</UL>
<P>The different reaction styles use these values in different ways, as
explained above.
</P>
<HR>

<P>If the ambipolar approximation is being used, via the <A HREF = "fix_ambipolar.html">fix
ambipolar</A> command, then reactions which involve
either ambipolar ions or the ambipolar electron have more restricitve
rules about the ordering of reactants and products, than those
described in the preceeding section.
</P>
<P>Note that ambipolar collisions are turned on via the <A HREF = "collide_modify.html">collide_modify
ambipolar yes</A> commands, which in turn requries
that the <A HREF = "fix_ambipolar.hmtl">fix ambipolar</A> is defined in your input
script.  This fix defines a particular species as an ambipolar
electron, written as "e" in the reactions that follow.  It also
defines a list of ambipolar ions, which are written as species with a
trailing "+" sign in the rules that follow.  Neutral species (without
"+") can be any non-ambipolar species.
</P>
<P>These rules only apply to reactions that involve ambipolar species
(ions or electrons) as a reactant or product.  Note that every
ambipolar reaction written here conserves charge.  I.e. the net charge
of the reactants equals the net charge of the products.
</P>
<P>Ambipolar dissociation reactions must list their reactants and
products in one of the following orders:
</P>
<PRE>AB + e -> A + e + B
AB+ + e -> A+ + e + B 
</PRE>
<P>Ambipolar ionization reactions with 2 or 3 products must be in one of
the following orders:
</P>
<PRE>A + B -> AB+ + e
A + e -> A+ + e + e 
</PRE>
<P>Ambipolar exchange reactions must be in one of the following orders:
</P>
<PRE>AB+ + e -> A + B
AB+ + C -> A + BC+
C + AB+ -> A + BC+ 
</PRE>
<P>Ambipolar recombination reactions must be in the following order:
</P>
<PRE>A+ + e -> A
A + B+ -> AB+
A+ + B -> AB+ 
</PRE>
<P>A third particle for recombination reactions can be specified in
the same way as described above for non-ambipolar recombination.
</P>
<HR>

<P>Styles with a <I>kk</I> suffix are functionally the same as the
corresponding style without the suffix.  They have been optimized to
run faster, depending on your available hardware, as discussed in the
<A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for different random number, round-off and
precision issues.
</P>
<P>These accelerated styles are part of the KOKKOS package. They are only
enabled if SPARTA was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
SPARTA</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke SPARTA, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See the <A HREF = "Section_accelerate.html">Accelerating SPARTA</A> section of the
manual for more instructions on how to use the accelerated styles
effectively.
</P>
<HR>

<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "collide.html">collide</A>, <A HREF = "surf_react.html">surf_react</A>
</P>
<P><B>Default:</B>
</P>
<P>style = none
</P>
<HR>

<A NAME = "Bird94"></A>

<P><B>(Bird94)</B> G. A. Bird, Molecular Gas Dynamics and the Direct
Simulation of Gas Flows, Clarendon Press, Oxford (1994).
</P>
<A NAME = "Bird09"></A>

<P><B>(Bird09)</B> G. A. Bird, Chemical Reactions in DSMC Rarefied Gas
Dynamics, Editor T Abe, AIP Conference Proceedings (2009).
</P>
<A NAME = "Bird11"></A>

<P><B>(Bird11)</B> G. A. Bird, "The Q-K model for gas-phase chemical reaction
rates", Physics of Fluids, 23, 106101, (2011).
</P>
<A NAME = "Gallis09"></A>

<P><B>(Gallis09)</B> M. A. Gallis, R. B. Bond, and J. R. Torczynski, "A
Kinetic-Theory Approach for Computing Chemical-Reaction Rates in
Upper-Atmosphere Hypersonic Flows", J Chem Phys, 131, 124311, (2009).
</P>
<A NAME = "Gallis11"></A>

<P><B>(Gallis10)</B> M. A. Gallis, R. B. Bond, and J. R.Torczynski,
"Assessment of Collision-Energy-Based Models for Atmospheric-Species
Reactions in Hypersonic Flows", J Thermophysics and Heat Transfer,
(2010).
</P>
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